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Data Processing/Variant data processing/process_HGMD_file.R

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+library(data.table)
+library(dplyr)
+library(tidyr)
+
+complement <- function(X){
+ if(X == 'A')
+ return('T')
+ else if(X == 'T')
+ return('A')
+ else if(X == 'C')
+ return('G')
+ else if(X == 'G')
+ return('C')
+}
+
+setwd("C:\\Users\\Azad\\OneDrive - UNSW\\Vafaee Lab\\Projects\\Deep Brain\\")
+dat <- fread("HGMD_Search_Results_PromoterActivity.txt") %>% as.data.frame() %>% dplyr::select(6,11)
+dat1 <- dat %>% tidyr::separate(1, c("SNP_chr","SNP_start","strand"), ":") %>% na.omit()
+dat1$SNP_end <- dat1$SNP_start
+dat2 <- (dat1 %>% tidyr::separate(4, c("X1","X2"), "\\["))[,-4] %>%
+ tidyr::separate(4, c("X3","X4"), "\\]") %>% dplyr::select(-5) %>% 
+ tidyr::separate(4, c("Ref","Alt"), "\\/")
+change <- which(dat2$strand == '-')
+dat3 = dat2
+dat3[change,4] <- sapply(dat3[change,4], function(x){
+ return(complement(x))
+})
+dat3[change,5] <- sapply(dat3[change,5], function(x){
+ return(complement(x))
+})
+dat3$SNP_id = paste0(dat3$SNP_chr, "_", dat3$SNP_start, "_", dat3$SNP_end)
+dat3 = dat3[,c("SNP_chr","SNP_start","SNP_end","SNP_id","Ref","Alt", "strand")]
+fwrite(dat3, file = "HGMD_Search_Results_PromoterActivity_processed.csv", sep = "\t", col.names = F)